Targets’ report corresponding to the functions that perform the full analysis, consisting in two parts:

  1. Annotate any original expression matrix (with gene symbols as ids in rows, and sample ids in columns) and expands the annotated matrix to include the average (or sum) values for the annotations (as new extra rows).

  2. Perform basic MFA analysis (as in “integrative_Analysis_MFA_v2.Rmd”) …

## Loading required package: plotly
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:MASS':
## 
##     select
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:AnnotationDbi':
## 
##     select
## The following object is masked from 'package:IRanges':
## 
##     slice
## The following object is masked from 'package:S4Vectors':
## 
##     rename
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
## Loading required package: viridis
## Loading required package: viridisLite
## 
## ======================
## Welcome to heatmaply version 1.3.0
## 
## Type citation('heatmaply') for how to cite the package.
## Type ?heatmaply for the main documentation.
## 
## The github page is: https://github.com/talgalili/heatmaply/
## Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
## You may ask questions at stackoverflow, use the r and heatmaply tags: 
##   https://stackoverflow.com/questions/tagged/heatmaply
## ======================
## 
## Attaching package: 'heatmaply'
## The following object is masked from 'package:BiocGenerics':
## 
##     normalize

Raw data (before data prep)

Data loaded from files data/mrna.csv and data/prots.csv

Samples in rows; Features in columns

## # A tibble: 150 x 201
##    sample  RTN2 NDRG2 CCDC113 FAM63A ACADS  GMDS HLA.H SEMA4A  ETS2 LIMD2  NME3  ZEB1 CDCP1 GIYD2 RTKN2 MANSC1
##    <chr>  <dbl> <dbl>   <dbl>  <dbl> <dbl> <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>
##  1 A0FJ    4.36  7.53   3.96    4.46  2.26  6.02  5.01   3.22  4.73  5.10  4.56  3.99  6.42  2.47  4.58   8.08
##  2 A13E    1.98  7.46   5.43    5.44  4.03  4.34  6.18   2.86  5.41  4.21  5.14  3.76  6.61  4.98  5.17   7.30
##  3 A0G0    1.73  8.08   2.23    5.54  2.63  6.36  6.04   5.95  5.65  3.30  4.45  3.85  6.41  3.20  4.24   7.99
##  4 A0SX    4.36  5.79   3.54    4.74  4.27  4.00  7.09   5.01  5.90  5.48  3.76  5.23  6.02  4.30  4.25   5.41
##  5 A143    2.45  7.16   4.69    4.81  2.44  7.03  5.94   5.90  6.64  5.51  4.24  3.54  7.09  5.71  3.96   8.49
##  6 A0DA    4.77  8.75   4.31    5.31  3.24  4.24  6.91   6.59  5.86  3.77  4.26  4.80  6.05  4.01  2.07   5.90
##  7 A0B3    3.35  5.10   0.593   5.22  3.89  5.92  8.04   6.53  6.31  4.11  4.79  4.26  7.27  4.64  3.53   5.03
##  8 A0I2    1.81  3.79   2.72    4.36  4.20  4.83  9.13   4.98  5.30  5.15  5.76  2.46  3.79  6.90  1.91   6.39
##  9 A0RT    2.09  6.33   2.36    4.04  4.13  4.29  7.59   5.94  6.57  7.07  5.13  5.55  3.85  5.66  4.27   3.71
## 10 A131    4.34  4.70   3.64    4.03  3.14  5.25  6.35   6.06  6.32  4.89  5.73  4.52  6.57  5.42  3.36   5.74
## # ... with 140 more rows, and 184 more variables: TAGLN <dbl>, IFIT3 <dbl>, ARL4C <dbl>, HTRA1 <dbl>,
## #   KIF13B <dbl>, CPPED1 <dbl>, SKAP2 <dbl>, ASPM <dbl>, KDM4B <dbl>, TBXAS1 <dbl>, MT1X <dbl>, MED13L <dbl>,
## #   SNORA8 <dbl>, RGS1 <dbl>, CBX6 <dbl>, WWC2 <dbl>, TNFRSF12A <dbl>, ZNF552 <dbl>, MAPRE2 <dbl>,
## #   SEMA5A <dbl>, STAT5A <dbl>, FLI1 <dbl>, COL15A1 <dbl>, C7orf55 <dbl>, ASF1B <dbl>, FUT8 <dbl>,
## #   LASS4 <dbl>, SQLE <dbl>, GPC4 <dbl>, AKAP12 <dbl>, AGL <dbl>, ADAMTS4 <dbl>, EPHB3 <dbl>, MAP3K1 <dbl>,
## #   PRNP <dbl>, PROM2 <dbl>, SLCO3A1 <dbl>, SNHG1 <dbl>, PRKCDBP <dbl>, MXI1 <dbl>, CSF1R <dbl>, TANC2 <dbl>,
## #   SLC19A2 <dbl>, RHOU <dbl>, C4orf34 <dbl>, LRIG1 <dbl>, DOCK8 <dbl>, BOC <dbl>, C11orf52 <dbl>, ...
## # A tibble: 150 x 112
##    sample   YWHAE EIF4EBP1 TP53BP1    ARAF   ACACA    ACCB  PRKAA1     ANLN     AR ARID1A   ASNS     ATM
##    <chr>    <dbl>    <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>    <dbl>  <dbl>  <dbl>  <dbl>   <dbl>
##  1 A0FJ    0.0491   0.447   0.918   0.0227 -0.0863 -0.417   0.285   0.172   -1.31   0.505  0.811 -0.496 
##  2 A13E   -0.0800   0.605   0.0591 -0.460  -0.593  -0.0623 -0.275   0.222   -1.62   0.340  1.18  -0.276 
##  3 A0G0   -0.0328   0.895   0.517  -0.192   0.411   0.826   0.0677  0.122   -1.08   0.227  1.95   0.771 
##  4 A0SX   -0.205   -0.141  -0.314  -0.0748 -0.851  -0.663   0.0296  1.05    -1.27   0.355  0.607  0.781 
##  5 A143    0.0602   0.132   0.331  -0.0244  0.770   0.873  -0.217   0.0138  -0.601  0.544  0.539  0.0139
##  6 A0DA    0.0308   0.0330 -0.220   0.419  -0.714  -0.218  -0.0631  0.0603  -1.21  -0.111  0.312  0.0717
##  7 A0B3   -0.108   -0.0371 -0.545   0.431  -0.363  -0.269  -0.0776  0.00887 -1.02  -0.233  1.14  -0.210 
##  8 A0I2    0.650   -0.521  -1.60   -0.187   1.08    1.59   -0.0775 -0.0519  -0.421 -0.355 -0.633 -0.924 
##  9 A0RT   -0.0137  -0.635  -0.721  -0.375  -1.25   -0.901  -0.178  -0.0419  -0.952 -0.179  0.145  0.834 
## 10 A131    0.431    1.05   -0.811   0.353  -0.883  -0.681   0.261  -0.00213 -0.180 -0.475  0.573 -1.44  
## # ... with 140 more rows, and 99 more variables: AKT1 <dbl>, ANXA1 <dbl>, BRAF <dbl>, BAK1 <dbl>, BAX <dbl>,
## #   BCL2 <dbl>, BCLX <dbl>, BECN1 <dbl>, BID <dbl>, BCL2L11 <dbl>, RAF1 <dbl>, PECAM1 <dbl>, ITGA2 <dbl>,
## #   CDK1 <dbl>, CASP7 <dbl>, CAV1 <dbl>, CHEK1 <dbl>, CHEK2 <dbl>, CLDN7 <dbl>, COL6A1 <dbl>, CCNB1 <dbl>,
## #   CCND1 <dbl>, CCNE1 <dbl>, PARK7 <dbl>, DVL3 <dbl>, CDH1 <dbl>, EGFR <dbl>, ESR1 <dbl>, MAPK1 <dbl>,
## #   FOXO3 <dbl>, FN1 <dbl>, GAB2 <dbl>, GATA3 <dbl>, GSK3A <dbl>, ERBB2 <dbl>, ERBB3 <dbl>, HSPA1A <dbl>,
## #   IGFBP2 <dbl>, INPP4B <dbl>, IRS1 <dbl>, MAPK9 <dbl>, MAPK8 <dbl>, KRAS <dbl>, XRCC5 <dbl>, LCK <dbl>,
## #   MAPK1_1 <dbl>, MAP2K1 <dbl>, ERRFI1 <dbl>, MRE11 <dbl>, CDH2 <dbl>, NF2 <dbl>, NOTCH1 <dbl>, ...

Data frame (before annotation)

Input from data/mrna.csv: Features in ROWS: 200 Samples in COLUMNS: 150

Input from data/prots.csv: Features in ROWS: 111 Samples in COLUMNS: 150

(Showing only partial output)

tar_read(dframe1)[1:10,1:10]
##             A0FJ     A13E     A0G0     A0SX     A143     A0DA      A0B3     A0I2     A0RT     A131
## RTN2    4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912
## NDRG2   7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056
## FAM63A  4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187
## ACADS   2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697
## GMDS    6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649
## HLA.H   5.006907 6.178668 6.039563 7.087633 5.936138 6.909727 8.0433411 9.130370 7.591606 6.349572
## SEMA4A  3.217812 2.864659 5.946028 5.007565 5.901459 6.591109 6.5328925 4.982386 5.941057 6.055191
## ETS2    4.734446 5.411029 5.651670 5.902449 6.641225 5.858016 6.3091167 5.304488 6.571389 6.317800
## LIMD2   5.099598 4.211397 3.304513 5.479451 5.508654 3.766283 4.1138727 5.149344 7.071896 4.885183
tar_read(dframe2)[1:10,1:10]
##                 A0FJ        A13E        A0G0        A0SX        A143        A0DA         A0B3        A0I2
## YWHAE     0.04913078 -0.07998211 -0.03284989 -0.20532949  0.06019021  0.03076171 -0.107861537  0.64984396
## EIF4EBP1  0.44748623  0.60521842  0.89460973 -0.14132292  0.13176899  0.03299680 -0.037124691 -0.52148657
## TP53BP1   0.91783419  0.05910121  0.51704453 -0.31372867  0.33091238 -0.22027100 -0.544743061 -1.60203535
## ARAF      0.02274147 -0.45985298 -0.19182192 -0.07482347 -0.02435747  0.41861665  0.430503500 -0.18714658
## ACACA    -0.08626782 -0.59269183  0.41117190 -0.85148060  0.76975143 -0.71430870 -0.363474049  1.07761482
## ACCB     -0.41662442 -0.06226840  0.82582859 -0.66341044  0.87347870 -0.21752677 -0.269313837  1.58998239
## PRKAA1    0.28527039 -0.27523360  0.06774184  0.02956373 -0.21653182 -0.06306506 -0.077581092 -0.07753959
## ANLN      0.17231110  0.22210598  0.12199399  1.05494810  0.01378422  0.06025690  0.008872461 -0.05187936
## AR       -1.30760569 -1.62047596 -1.07789444 -1.26705469 -0.60132744 -1.20803848 -1.016297633 -0.42122691
## ARID1A    0.50509449  0.33958160  0.22718066  0.35529767  0.54412514 -0.11094480 -0.233223615 -0.35537533
##                 A0RT         A131
## YWHAE    -0.01365044  0.430934243
## EIF4EBP1 -0.63485063  1.052571622
## TP53BP1  -0.72072329 -0.811335319
## ARAF     -0.37488300  0.353262354
## ACACA    -1.25449108 -0.883296744
## ACCB     -0.90135358 -0.681364747
## PRKAA1   -0.17763665  0.261182525
## ANLN     -0.04188024 -0.002134606
## AR       -0.95232486 -0.180283541
## ARID1A   -0.17919526 -0.474665632

Heatmaps (before annotation)

Features in ROWS; Samples in COLUMNS

Heatmaply

p <- heatmaply(data.matrix(dframe1), 
        #dendrogram = "row",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(data.matrix(dframe1)),
        labRow = rownames(data.matrix(dframe1)),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")
p <- heatmaply(data.matrix(dframe2), 
        #dendrogram = "row",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(data.matrix(dframe2)),
        labRow = rownames(data.matrix(dframe2)),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")

Annotated Matrix

Gene Ontology used: BP

Min. number of genes required to pass the filter: 8

Annotated categories: 13 (for data/mrna.csv)

Annotated categories: 61 (for data/prots.csv)

Shared annotated categories: GO:0000122, GO:0006357, GO:0007155, GO:0007165, GO:0007411, GO:0008285, GO:0019221, GO:0030335, GO:0045893, GO:0045944

(Showing only partial output)

tar_read(categ_sums1)
## GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0016477 GO:0019221 GO:0030335 GO:0043312 
##         11         14         11         21         10          9         10         10          8          8 
## GO:0045893 GO:0045944 GO:0055114 
##         11         14         10
tar_read(categ_sums2)
## GO:0000082 GO:0000122 GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001701 GO:0001934 GO:0006357 GO:0006367 
##          8         19         17          8         11          9         10         10         13         10 
## GO:0006468 GO:0006915 GO:0006974 GO:0006977 GO:0007050 GO:0007155 GO:0007165 GO:0007169 GO:0007411 GO:0007507 
##         24         17         14          8         10         11         30         11          8         12 
## GO:0007568 GO:0008283 GO:0008284 GO:0008285 GO:0010468 GO:0010628 GO:0010629 GO:0016032 GO:0016579 GO:0018105 
##         10         12         20         16          8         29         12         19         11         16 
## GO:0018107 GO:0018108 GO:0019221 GO:0030154 GO:0030335 GO:0032355 GO:0032869 GO:0033138 GO:0033674 GO:0035556 
##         11         11         15         11         11         10          9          9          8         17 
## GO:0042060 GO:0042127 GO:0042493 GO:0042981 GO:0043065 GO:0043066 GO:0045471 GO:0045892 GO:0045893 GO:0045944 
##          9          9         23         10         11         31          8         11         23         30 
## GO:0046777 GO:0048538 GO:0050821 GO:0051091 GO:0051897 GO:0070374 GO:0071456 GO:0090090 GO:0098609 GO:1901796 
##         10          8          8          8         12          9         11          8          9          9 
## GO:2001244 
##          8
head(tar_read(categ_intersect1))
##         GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## RTN2             0          0          0          0          0          0          0          0          0
## NDRG2            0          0          0          1          0          0          0          0          0
## CCDC113          0          0          0          0          0          0          0          0          0
## FAM63A           0          0          0          0          0          0          0          0          0
## ACADS            0          0          0          0          0          0          0          0          0
## GMDS             0          0          0          0          0          0          0          0          0
##         GO:0045944
## RTN2             0
## NDRG2            0
## CCDC113          0
## FAM63A           0
## ACADS            0
## GMDS             0
head(tar_read(categ_intersect2))
##          GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## YWHAE             0          0          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          0          0          0          0          0          0          0          1
## ARAF              0          0          0          0          0          0          0          0          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0045944
## YWHAE             0
## EIF4EBP1          0
## TP53BP1           1
## ARAF              0
## ACACA             0
## ACCB              0
tar_read(categ_intersect)
##           GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## RTN2               0          0          0          0          0          0          0          0          0
## NDRG2              0          0          0          1          0          0          0          0          0
## CCDC113            0          0          0          0          0          0          0          0          0
## FAM63A             0          0          0          0          0          0          0          0          0
## ACADS              0          0          0          0          0          0          0          0          0
## GMDS               0          0          0          0          0          0          0          0          0
## HLA.H              0          0          0          0          0          0          0          0          0
## SEMA4A             0          0          0          0          1          0          0          1          0
## ETS2               1          1          0          0          0          0          0          0          1
## LIMD2              0          0          0          0          0          0          0          0          0
## NME3               0          0          0          0          0          0          0          0          0
## ZEB1               1          1          0          0          0          1          1          0          0
## CDCP1              0          0          0          0          0          0          0          0          0
## GIYD2              0          0          0          0          0          0          0          0          0
## RTKN2              0          0          0          1          0          0          0          0          0
## MANSC1             0          0          0          0          0          0          0          0          0
## TAGLN              0          0          0          0          0          0          0          0          0
## IFIT3              0          0          0          0          0          1          0          0          0
## ARL4C              0          0          0          0          0          0          0          0          0
## HTRA1              0          0          0          0          0          0          0          0          0
## KIF13B             0          0          0          1          0          0          0          0          0
## CPPED1             0          0          0          0          0          0          0          0          0
## SKAP2              0          0          0          1          0          1          0          0          0
## ASPM               0          0          0          0          0          0          0          0          0
## KDM4B              0          0          0          0          0          0          0          0          0
## TBXAS1             0          0          0          0          0          0          0          0          0
## MT1X               0          0          0          0          0          0          0          0          0
## MED13L             0          1          0          0          0          0          0          0          0
## SNORA8             0          0          0          0          0          0          0          0          0
## RGS1               0          0          0          1          0          0          0          0          0
## CBX6               1          0          0          0          0          0          0          0          0
## WWC2               1          0          0          0          0          0          0          0          0
## TNFRSF12A          0          0          0          0          0          0          0          0          0
## ZNF552             0          1          0          0          0          0          0          0          0
## MAPRE2             0          0          0          0          0          0          0          0          0
## SEMA5A             0          0          1          0          1          0          0          1          0
## STAT5A             0          1          0          0          0          0          1          0          0
## FLI1               0          1          0          0          0          0          0          0          1
## COL15A1            0          0          1          1          0          0          0          0          0
## C7orf55            0          0          0          0          0          0          0          0          0
## ASF1B              0          0          0          0          0          0          0          0          0
## FUT8               0          0          0          0          0          0          0          0          0
## LASS4              0          0          0          0          0          0          0          0          0
## SQLE               0          0          0          0          0          0          0          0          0
## GPC4               0          0          0          0          0          0          0          0          0
## AKAP12             0          0          0          0          0          0          0          0          0
## AGL                0          0          0          0          0          0          0          0          0
## ADAMTS4            0          0          0          0          0          0          0          0          0
## EPHB3              0          0          0          0          1          0          0          0          0
## MAP3K1             0          0          0          0          0          0          0          0          0
## PRNP               0          0          0          0          0          0          0          0          0
## PROM2              0          0          0          0          0          0          0          0          0
## SLCO3A1            0          0          0          0          0          0          0          0          0
## SNHG1              0          0          0          0          0          0          0          0          0
## PRKCDBP            0          0          0          0          0          0          0          0          0
## MXI1               1          0          0          0          0          0          0          0          0
## CSF1R              0          0          0          1          1          1          1          1          0
## TANC2              0          0          0          0          0          0          0          0          0
## SLC19A2            0          0          0          0          0          0          0          0          0
## RHOU               0          0          0          0          0          0          1          0          0
## C4orf34            0          0          0          0          0          0          0          0          0
## LRIG1              0          0          0          0          0          0          0          0          0
## DOCK8              0          0          0          0          0          0          0          0          0
## BOC                0          0          1          0          1          0          0          0          0
## C11orf52           0          0          0          0          0          0          0          0          0
## S100A16            0          0          0          0          0          0          0          0          0
## NRARP              1          0          0          0          0          0          0          0          0
## TTC23              0          0          0          0          0          0          0          0          0
## TBC1D4             0          0          0          0          0          0          0          0          0
## DEPDC6             0          0          0          0          0          0          0          0          0
## ILDR1              0          0          0          0          0          0          0          0          0
## SDC1               0          0          0          0          0          0          1          0          0
## STC2               0          0          0          0          0          0          0          0          0
## DTWD2              0          0          0          0          0          0          0          0          0
## TCF4               0          0          0          0          0          0          0          0          1
## ITPR2              0          0          0          1          0          0          0          0          0
## DPYD               0          0          0          0          0          0          0          0          0
## NME1               0          0          0          0          0          1          0          0          0
## EGLN3              0          0          0          0          0          0          0          0          0
## CD302              0          0          0          0          0          0          0          0          0
## AHR                1          1          0          0          0          0          0          0          1
## LAPTM4B            0          0          0          0          0          0          0          0          0
## OCLN               0          0          0          0          0          0          0          0          0
## HIST1H2BK          0          0          0          0          0          0          0          0          0
## HDAC11             0          0          0          0          0          0          0          0          0
## C18orf1            0          0          0          0          0          0          0          0          0
## C6orf192           0          0          0          0          0          0          0          0          0
## AMPD3              0          0          0          0          0          0          0          0          0
## COL6A1             0          0          1          0          0          0          0          0          0
## RAB3IL1            0          0          0          0          0          0          0          0          0
## APBB1IP            0          0          0          1          0          0          0          0          0
## PSIP1              0          1          0          0          0          0          0          0          0
## EIF2AK2            0          0          0          0          0          1          0          0          0
## CSRP2              0          0          0          0          0          0          0          0          0
## EIF4EBP3           0          0          0          0          0          0          0          0          0
## LYN                0          0          0          1          0          1          0          1          0
## WDR76              0          0          0          0          0          0          0          0          0
## SAMD9L             0          0          0          0          0          0          0          0          0
## ASPH               0          0          0          0          0          1          0          0          0
## RBL1               1          0          0          0          0          0          0          0          0
## SLC43A3            0          0          0          0          0          0          0          0          0
## HN1                0          0          0          0          0          0          0          0          0
## TTC39A             0          0          0          0          0          0          0          0          0
## MTL5               0          0          0          0          0          0          0          0          0
## NES                0          0          0          0          0          0          0          0          0
## APOD               0          0          0          0          0          0          0          0          0
## RIN3               0          0          0          1          0          0          0          0          0
## ALCAM              0          0          1          1          0          0          0          0          0
## C1orf38            0          0          0          0          0          0          0          0          0
## PLCD3              0          0          0          0          0          0          0          0          0
## BSPRY              0          0          0          0          0          0          0          0          0
## NTN4               0          0          0          0          1          0          0          0          0
## IL1R1              0          0          0          0          0          0          1          0          0
## EMP3               0          0          0          0          0          0          0          0          0
## ZKSCAN1            0          1          0          0          0          0          0          0          0
## FMNL2              0          0          0          0          0          0          0          0          0
## OGFRL1             0          0          0          0          0          0          0          0          0
## IRF5               0          0          0          0          0          0          0          0          0
## IGSF3              0          0          0          0          0          0          0          0          0
## DBP                0          1          0          0          0          0          0          0          0
## CNN2               0          0          0          0          0          0          0          0          0
## CAMK2D             0          1          0          0          0          0          0          0          0
## SIGIRR             0          0          0          1          0          0          0          0          0
## AKAP9              0          0          0          1          0          0          0          0          0
## ICA1               0          0          0          0          0          0          0          0          0
## FGD5               0          0          0          0          0          0          0          0          0
## DSG2               0          0          1          0          0          0          0          0          0
## E2F1               1          0          0          0          0          0          0          0          1
## QSOX1              0          0          0          0          0          0          0          0          0
## TOB1               0          0          0          0          0          1          0          0          0
## CSF3R              0          0          1          1          0          0          1          0          0
## SHROOM3            0          0          0          0          0          0          0          0          0
## CCDC80             0          0          0          0          0          0          0          0          0
## FRMD6              0          0          0          0          0          0          0          0          0
## CXCL12             0          0          1          1          1          0          0          1          0
## CCNA2              0          0          0          0          0          0          0          0          1
## TIGD5              0          0          0          0          0          0          0          0          0
## ALDH6A1            0          0          0          0          0          0          0          0          0
## POSTN              0          0          1          0          0          0          0          0          0
## FZD4               0          0          0          0          0          0          1          0          1
## NCAPG2             0          0          0          0          0          0          0          0          0
## SDC4               0          0          0          0          0          0          0          0          0
## SNED1              0          0          0          0          0          0          0          0          0
## PLEKHA4            0          0          0          0          0          0          0          0          0
## KCNAB2             0          0          0          0          0          0          0          0          0
## SH3KBP1            0          0          0          0          1          0          0          0          0
## IGSF9              0          0          0          0          1          0          0          0          0
## DNLZ               0          0          0          0          0          0          0          0          0
## S1PR3              0          0          0          0          0          0          0          0          0
## PTPRE              0          0          0          0          0          0          0          0          0
## FLJ23867           0          0          0          0          0          0          0          0          0
## PLSCR1             0          0          0          0          0          0          0          0          0
## LMO4               0          0          0          0          0          0          0          0          0
## IFITM2             0          0          0          0          0          0          0          0          0
## LRRC25             0          0          0          0          0          0          0          0          0
## TST                0          0          0          0          0          0          0          0          0
## NCF4               0          0          0          0          0          0          0          0          0
## NCOA7              0          0          0          0          0          0          0          0          0
## IL4R               0          0          0          1          0          0          1          0          0
## CCDC64B            0          0          0          0          0          0          0          0          0
## SGPP1              0          0          0          0          0          0          0          0          0
## RUNX3              1          1          0          0          0          0          0          0          1
## SLC5A6             0          0          0          0          0          0          0          0          0
## IFIH1              0          0          0          0          0          0          0          0          0
## PREX1              0          0          0          0          0          0          0          1          0
## PLAUR              0          0          0          1          0          0          0          0          0
## CDK18              0          0          0          0          0          0          0          0          0
## SLC43A2            0          0          0          0          0          0          0          0          0
## GK                 0          0          0          0          0          0          0          0          0
## ICAM2              0          0          1          0          0          0          0          0          0
## YPEL2              0          0          0          0          0          0          0          0          0
## CBR1               0          0          0          0          0          0          0          0          0
## MEX3A              0          0          0          0          0          0          0          0          0
## ZNRF3              0          0          0          0          0          0          0          0          0
## PTPRM              0          0          0          1          0          0          0          0          0
## C1orf162           0          0          0          0          0          0          0          0          0
## GAS6               0          0          0          1          0          0          0          0          0
## C1QB               0          0          0          0          0          0          0          0          0
## PVRL4              0          0          0          0          0          0          0          0          0
## CTSK               0          0          0          0          0          0          0          0          0
## MRVI1              0          0          0          0          0          0          0          0          0
## LEF1               1          0          0          0          0          0          0          1          1
## PLCD4              0          0          0          0          0          0          0          0          0
## ZNF37B             0          0          0          0          0          0          0          0          0
## MEGF9              0          0          0          0          0          0          0          0          0
## GINS2              0          0          0          0          0          0          0          0          0
## FAM13A             0          0          0          1          0          0          0          0          0
## CPT1A              0          0          0          0          0          0          0          0          0
## SNX10              0          0          0          0          0          0          0          0          0
## TRIM45             0          0          0          0          0          0          0          0          1
## ELP2               0          1          0          0          0          0          0          0          0
## ALOX5              0          0          0          0          0          0          1          0          0
## AMN1               0          0          0          0          0          0          0          0          0
## CERCAM             0          0          1          0          0          0          0          0          0
## SEMA3C             0          0          0          0          1          0          0          1          0
## KRT8               0          0          0          0          0          0          0          0          0
## TP53INP2           0          0          0          0          0          0          0          0          1
## JAM3               0          0          0          0          0          0          0          0          0
## ZNF680             0          0          0          0          0          0          0          0          0
## PBX1               0          1          0          0          0          0          0          0          0
## YWHAE              0          0          0          0          0          0          0          0          0
## EIF4EBP1           0          0          0          0          0          0          0          0          0
## TP53BP1            0          0          0          0          0          0          0          0          1
## ARAF               0          0          0          0          0          0          0          0          0
## ACACA              0          0          0          0          0          0          0          0          0
## ACCB               0          0          0          0          0          0          0          0          0
## PRKAA1             0          0          0          1          0          0          0          0          0
## ANLN               0          0          0          0          0          0          0          0          0
## AR                 1          1          0          1          0          1          0          0          1
## ARID1A             1          1          0          0          0          0          0          0          1
## ASNS               0          0          0          0          0          0          0          0          0
## ATM                0          0          0          1          0          0          0          1          0
## AKT1               0          0          0          1          0          0          1          0          1
## ANXA1              0          0          0          1          0          0          1          0          0
## BRAF               0          0          0          0          0          0          0          0          0
## BAK1               0          0          0          0          0          1          0          0          0
## BAX                0          0          0          0          0          0          0          0          0
## BCL2               0          0          0          0          0          0          1          0          0
## BCLX               0          0          0          0          0          0          0          0          0
## BECN1              0          0          0          0          0          0          0          0          0
## BID                0          0          0          0          0          0          0          0          0
## BCL2L11            0          0          0          0          0          0          0          0          0
## RAF1               0          0          0          1          0          1          0          0          0
## PECAM1             0          0          0          1          0          0          0          1          0
## ITGA2              0          0          1          0          0          0          0          0          0
## CDK1               0          0          0          0          0          0          0          0          0
## CASP7              0          0          0          0          0          0          0          0          0
## CAV1               1          0          0          0          0          0          0          1          0
## CHEK1              0          0          0          0          0          0          0          0          0
## CHEK2              0          0          0          0          0          0          0          0          1
## CLDN7              0          0          1          0          0          0          0          0          0
## COL6A1             0          0          1          0          0          0          0          0          0
## CCNB1              0          0          0          0          0          0          0          0          0
## CCND1              1          0          0          0          0          0          1          0          0
## CCNE1              1          0          0          0          0          0          0          0          0
## PARK7              0          0          0          0          0          0          0          0          0
## DVL3               0          0          0          0          0          0          0          0          1
## CDH1               0          0          0          0          0          0          0          0          1
## EGFR               0          1          0          1          0          0          0          1          1
## ESR1               1          1          0          1          0          0          0          0          1
## MAPK1              0          0          0          1          1          0          0          0          1
## FOXO3              1          1          0          0          0          0          1          0          1
## FN1                0          0          1          0          0          0          1          0          0
## GAB2               0          0          0          0          1          0          1          0          0
## GATA3              1          0          0          1          1          1          1          0          1
## GSK3A              0          0          0          1          0          0          0          0          0
## ERBB2              0          1          0          1          0          0          0          0          0
## ERBB3              0          0          0          1          0          0          0          0          0
## HSPA1A             0          0          0          0          0          1          0          0          0
## IGFBP2             0          0          0          1          0          0          0          0          0
## INPP4B             0          0          0          1          0          0          0          0          0
## IRS1               0          0          0          1          0          0          0          0          0
## MAPK9              0          0          0          0          0          0          0          0          0
## MAPK8              0          0          0          0          0          0          0          0          0
## KRAS               0          0          0          0          0          0          1          0          0
## XRCC5              0          0          0          0          0          0          0          0          0
## LCK                0          0          0          0          0          0          0          0          0
## MAPK1_1            0          0          0          0          0          0          0          0          0
## MAP2K1             0          0          0          1          0          1          0          0          1
## ERRFI1             0          0          0          0          0          0          0          0          0
## MRE11              0          0          0          0          0          0          0          0          0
## CDH2               0          0          1          0          0          0          0          0          0
## NF2                0          0          0          0          0          1          0          0          0
## NOTCH1             1          0          0          0          1          1          0          1          1
## CDH3               0          0          1          0          0          0          0          0          0
## SERPINE1           0          0          0          0          0          0          0          0          0
## PCNA               1          0          0          0          0          0          0          0          0
## PDCD4              0          0          0          0          0          0          0          0          0
## PDK1               0          0          0          0          0          0          0          0          0
## PRKCA              0          0          1          0          1          0          0          1          0
## PRKCD              0          0          0          1          0          0          0          0          0
## PGR                0          1          0          1          0          0          0          0          0
## AKT1S1             0          0          0          0          0          0          0          0          0
## PRDX1              0          0          0          0          0          0          0          0          0
## PTEN               0          0          0          0          0          1          0          0          0
## PXN                0          0          1          1          0          0          0          0          0
## PEA15              0          0          0          0          0          0          0          0          0
## RBM3               0          0          0          0          0          0          0          0          0
## RAD50              0          0          0          0          0          0          0          0          0
## RB1                1          0          0          0          0          0          0          0          0
## CD1E               0          0          0          0          0          0          0          0          0
## STAT3              1          1          0          1          0          1          1          1          1
## STAT5A             0          1          0          0          0          0          1          0          0
## SHC1               0          0          0          0          1          0          1          0          1
## SMAD1              1          0          0          1          0          1          0          0          0
## SMAD3              1          1          0          0          0          0          0          1          1
## SMAD4              1          0          0          0          1          1          0          0          1
## SRC                0          0          1          1          1          0          0          0          1
## STMN1              0          0          0          1          0          0          0          0          0
## SYK                0          0          0          0          0          0          0          0          0
## TGM1               0          0          0          0          0          0          0          0          0
## TSC2               0          0          0          0          0          1          0          0          0
## KDR                0          0          0          0          0          0          0          1          0
## XBP1               0          0          0          0          0          0          0          1          0
## XRCC1              0          0          0          0          0          0          0          0          0
## YAP1               0          0          0          0          0          0          0          0          1
## YBX1               1          0          0          0          0          0          0          0          0
## CTNNA1             0          0          1          0          0          0          0          0          0
## CTNNB1             1          0          1          0          0          1          0          0          1
## KIT                0          1          0          1          0          0          1          1          0
## MET                0          0          0          1          0          0          0          0          0
## MYC                1          1          0          0          0          0          1          0          1
## EEF2               0          0          0          0          0          0          0          0          0
## EEF2K              0          0          0          0          0          0          0          0          0
## EIF4E              0          0          0          0          0          0          0          0          0
## MTOR               0          0          0          0          0          0          0          0          0
## CDKN1B             0          0          0          0          0          1          0          0          0
## MAPK14             0          1          0          1          0          0          0          0          0
## TP53               1          0          0          0          0          1          1          0          1
## RPS6KB1            0          0          0          1          0          0          0          0          0
## RPS6KA1            0          0          0          1          0          0          0          0          0
##           GO:0045944
## RTN2               0
## NDRG2              0
## CCDC113            0
## FAM63A             0
## ACADS              0
## GMDS               0
## HLA.H              0
## SEMA4A             0
## ETS2               1
## LIMD2              0
## NME3               0
## ZEB1               1
## CDCP1              0
## GIYD2              0
## RTKN2              0
## MANSC1             0
## TAGLN              0
## IFIT3              0
## ARL4C              0
## HTRA1              0
## KIF13B             0
## CPPED1             0
## SKAP2              0
## ASPM               0
## KDM4B              0
## TBXAS1             0
## MT1X               0
## MED13L             0
## SNORA8             0
## RGS1               0
## CBX6               0
## WWC2               0
## TNFRSF12A          0
## ZNF552             0
## MAPRE2             0
## SEMA5A             0
## STAT5A             1
## FLI1               1
## COL15A1            0
## C7orf55            0
## ASF1B              0
## FUT8               0
## LASS4              0
## SQLE               0
## GPC4               0
## AKAP12             0
## AGL                0
## ADAMTS4            0
## EPHB3              0
## MAP3K1             0
## PRNP               0
## PROM2              0
## SLCO3A1            0
## SNHG1              0
## PRKCDBP            0
## MXI1               0
## CSF1R              0
## TANC2              0
## SLC19A2            0
## RHOU               0
## C4orf34            0
## LRIG1              0
## DOCK8              0
## BOC                0
## C11orf52           0
## S100A16            0
## NRARP              0
## TTC23              0
## TBC1D4             0
## DEPDC6             0
## ILDR1              0
## SDC1               0
## STC2               0
## DTWD2              0
## TCF4               1
## ITPR2              0
## DPYD               0
## NME1               0
## EGLN3              0
## CD302              0
## AHR                1
## LAPTM4B            0
## OCLN               0
## HIST1H2BK          0
## HDAC11             0
## C18orf1            0
## C6orf192           0
## AMPD3              0
## COL6A1             0
## RAB3IL1            0
## APBB1IP            0
## PSIP1              0
## EIF2AK2            0
## CSRP2              0
## EIF4EBP3           0
## LYN                0
## WDR76              0
## SAMD9L             0
## ASPH               0
## RBL1               1
## SLC43A3            0
## HN1                0
## TTC39A             0
## MTL5               0
## NES                0
## APOD               0
## RIN3               0
## ALCAM              0
## C1orf38            0
## PLCD3              0
## BSPRY              0
## NTN4               0
## IL1R1              0
## EMP3               0
## ZKSCAN1            0
## FMNL2              0
## OGFRL1             0
## IRF5               1
## IGSF3              0
## DBP                1
## CNN2               0
## CAMK2D             0
## SIGIRR             0
## AKAP9              0
## ICA1               0
## FGD5               0
## DSG2               0
## E2F1               1
## QSOX1              0
## TOB1               0
## CSF3R              0
## SHROOM3            0
## CCDC80             0
## FRMD6              0
## CXCL12             0
## CCNA2              0
## TIGD5              0
## ALDH6A1            0
## POSTN              0
## FZD4               0
## NCAPG2             0
## SDC4               0
## SNED1              0
## PLEKHA4            0
## KCNAB2             0
## SH3KBP1            0
## IGSF9              0
## DNLZ               0
## S1PR3              0
## PTPRE              0
## FLJ23867           0
## PLSCR1             1
## LMO4               1
## IFITM2             0
## LRRC25             0
## TST                0
## NCF4               0
## NCOA7              1
## IL4R               0
## CCDC64B            0
## SGPP1              0
## RUNX3              0
## SLC5A6             0
## IFIH1              0
## PREX1              0
## PLAUR              0
## CDK18              0
## SLC43A2            0
## GK                 0
## ICAM2              0
## YPEL2              0
## CBR1               0
## MEX3A              0
## ZNRF3              0
## PTPRM              0
## C1orf162           0
## GAS6               0
## C1QB               0
## PVRL4              0
## CTSK               0
## MRVI1              0
## LEF1               1
## PLCD4              0
## ZNF37B             0
## MEGF9              0
## GINS2              0
## FAM13A             0
## CPT1A              0
## SNX10              0
## TRIM45             0
## ELP2               0
## ALOX5              0
## AMN1               0
## CERCAM             0
## SEMA3C             0
## KRT8               0
## TP53INP2           0
## JAM3               0
## ZNF680             0
## PBX1               0
## YWHAE              0
## EIF4EBP1           0
## TP53BP1            1
## ARAF               0
## ACACA              0
## ACCB               0
## PRKAA1             0
## ANLN               0
## AR                 1
## ARID1A             0
## ASNS               0
## ATM                1
## AKT1               1
## ANXA1              0
## BRAF               0
## BAK1               0
## BAX                0
## BCL2               0
## BCLX               0
## BECN1              0
## BID                0
## BCL2L11            0
## RAF1               1
## PECAM1             0
## ITGA2              0
## CDK1               0
## CASP7              0
## CAV1               0
## CHEK1              0
## CHEK2              0
## CLDN7              0
## COL6A1             0
## CCNB1              0
## CCND1              0
## CCNE1              0
## PARK7              1
## DVL3               1
## CDH1               0
## EGFR               1
## ESR1               1
## MAPK1              0
## FOXO3              1
## FN1                0
## GAB2               0
## GATA3              1
## GSK3A              1
## ERBB2              0
## ERBB3              0
## HSPA1A             0
## IGFBP2             0
## INPP4B             0
## IRS1               0
## MAPK9              0
## MAPK8              0
## KRAS               0
## XRCC5              0
## LCK                0
## MAPK1_1            0
## MAP2K1             0
## ERRFI1             0
## MRE11              0
## CDH2               0
## NF2                0
## NOTCH1             1
## CDH3               0
## SERPINE1           1
## PCNA               0
## PDCD4              0
## PDK1               0
## PRKCA              0
## PRKCD              0
## PGR                1
## AKT1S1             0
## PRDX1              0
## PTEN               0
## PXN                0
## PEA15              0
## RBM3               0
## RAD50              0
## RB1                1
## CD1E               0
## STAT3              1
## STAT5A             1
## SHC1               0
## SMAD1              1
## SMAD3              1
## SMAD4              1
## SRC                0
## STMN1              0
## SYK                0
## TGM1               0
## TSC2               0
## KDR                0
## XBP1               1
## XRCC1              0
## YAP1               1
## YBX1               1
## CTNNA1             0
## CTNNB1             1
## KIT                0
## MET                1
## MYC                1
## EEF2               0
## EEF2K              0
## EIF4E              0
## MTOR               0
## CDKN1B             0
## MAPK14             1
## TP53               1
## RPS6KB1            0
## RPS6KA1            1

Features in ROWS: 200 (for data/mrna.csv)

Features in ROWS: 111 (for data/prots.csv)

Samples+Categs in COLUMNS: 163 (for data/mrna.csv)

Samples+Categs in COLUMNS: 211 (for data/prots.csv)

(Showing only partial output)

head(tar_read(annot_matrix1))
##             A0FJ     A13E     A0G0     A0SX     A143     A0DA      A0B3     A0I2     A0RT     A131     A124
## RTN2    4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912 1.206280
## NDRG2   7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950 8.676364
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056 3.753526
## FAM63A  4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187 5.193696
## ACADS   2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697 2.789757
## GMDS    6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649 5.610192
##             A1B6     A1AZ     A0YM     A04P     A04T     A0AT      A0AL     A0CE     A07R      A0FL     A150
## RTN2    2.846980 1.222353 1.892681 2.293955 1.090914 2.534021 2.4179929 1.763550 3.280434  6.142850 2.308591
## NDRG2   7.790635 4.730645 6.332405 7.827413 7.436516 6.961400 8.8336442 6.544614 6.875960 10.260165 5.887077
## CCDC113 3.060775 4.506151 3.208926 1.881223 3.664815 3.319350 0.2849741 4.309775 2.222412  1.441558 3.790442
## FAM63A  3.819955 4.464141 4.559118 3.709155 5.139812 3.491093 4.6556456 5.179804 5.368074  5.961550 4.274774
## ACADS   4.125045 3.028432 3.393146 2.456713 2.409692 1.834359 4.2644283 3.688115 3.009596  3.850541 3.018863
## GMDS    5.601640 4.144106 4.708556 6.716958 5.173432 5.728591 5.7582700 5.420492 4.877815  6.642912 5.163194
##              A0E0     A0U4     A0XU     A0AV     A0AR     A0RX     A0D2     A0CM     A0WX     A0T0     A0T2
## RTN2    0.6743217 2.218695 3.320557 3.690360 2.910988 2.179577 1.965177 1.903714 3.070428 2.360129 3.620557
## NDRG2   4.5619890 7.385044 7.341238 5.753302 9.515500 7.047445 6.725903 4.983993 6.789360 9.155272 7.013197
## CCDC113 2.2716035 4.860181 4.620859 2.898493 2.883201 3.553867 1.249060 1.779161 4.790587 4.160914 3.172523
## FAM63A  6.0971133 3.800083 4.955763 5.765022 4.940644 4.360755 3.873571 4.664145 4.569566 4.872187 4.834117
## ACADS   4.3603055 3.454774 2.629412 2.778064 4.266805 3.867138 2.698221 1.556919 3.506256 2.350685 4.589873
## GMDS    4.4246369 5.455150 5.699021 4.910252 7.105627 4.995109 5.584181 4.981640 4.736113 4.825226 5.816029
##             A04U     A0JL     A147     A0B9      A1AI     A14X     A12V     A1AY     A0D0     A0SK     A128
## RTN2    1.384660 3.243859 3.505726 2.650759 0.3327526 3.628534 2.813715 3.497809 1.949481 4.794359 1.957013
## NDRG2   8.911393 9.339442 7.000853 7.243034 7.5131668 8.894409 8.556629 5.543856 4.910012 4.484965 3.858092
## CCDC113 1.412959 3.440030 3.978750 3.947715 4.1002872 2.966176 2.243080 4.186226 3.734065 3.500417 4.236216
## FAM63A  3.002935 4.850530 5.789872 4.526164 4.4563209 6.017519 4.719815 5.140818 2.203462 4.008493 1.840127
## ACADS   4.236686 3.006019 2.561543 3.478710 2.1922975 3.740005 3.446792 3.021059 3.308981 3.099769 3.204864
## GMDS    4.715617 5.033427 3.392365 4.530231 5.4230176 6.103145 4.414810 5.021890 4.402124 3.941773 5.958135
##             A04D     A0A7     A094     A12L     A0I9      A0EE     A135     A152     A18P     A18R     A08X
## RTN2    3.264143 3.630609 3.838779 2.836670 4.724076 0.6962941 1.819296 1.986657 3.475001 4.354183 3.733788
## NDRG2   9.645246 5.026081 5.260215 3.344884 4.503244 5.8202163 5.403551 4.999541 4.823776 6.402254 4.675284
## CCDC113 3.930012 2.450502 1.773722 5.404862 4.622169 3.1173445 4.118666 3.577636 4.374714 3.983280 3.294215
## FAM63A  5.762041 3.948055 3.928293 5.957079 5.570075 3.9983956 4.021509 5.645919 5.640225 4.190554 3.351270
## ACADS   3.045266 3.193824 4.305221 3.095219 4.583606 3.0785379 2.832452 2.867549 3.070213 5.606610 3.359589
## GMDS    5.038067 4.443301 5.812546 5.134322 4.819258 6.7714094 3.013772 3.917772 3.582233 2.518043 4.138523
##             A0TX     A09X     A1AT     A12Q     A12T     A0RH     A07I     A04W     A12P     A0EQ      A0D1
## RTN2    2.931286 1.973935 4.178227 2.454749 3.360365 3.105367 3.843009 2.413193 4.780633 2.043937 2.8101153
## NDRG2   6.297263 4.741524 4.883940 4.679603 3.993496 4.467796 3.360024 5.915364 3.728883 4.451327 5.8398955
## CCDC113 4.381832 1.385884 4.041319 5.460908 4.168762 3.280249 5.273710 4.304850 3.611869 3.922623 3.8977020
## FAM63A  4.210461 2.777252 5.143692 7.478075 4.102186 5.490180 6.218413 4.735519 5.428217 3.733726 4.5425832
## ACADS   3.222013 2.480992 2.690258 3.902902 3.739438 3.791578 1.207714 2.316943 4.292261 2.387349 0.8715574
## GMDS    4.649420 4.547114 4.445286 5.259775 4.632893 4.769685 5.248546 5.203775 2.470152 3.986822 6.0863133
##             A09G     A1B0     A14P     A0T1      A137     A13Z     A08L     A0IK     A12D     A0XN     A0B0
## RTN2    4.336523 2.460993 2.725320 3.987558 3.3557342 3.858600 3.683918 3.805449 4.913829 3.854908 2.937087
## NDRG2   5.890453 3.328238 4.519024 5.339332 4.1665630 5.779159 6.035885 5.045742 5.362417 4.280310 6.399544
## CCDC113 3.385647 5.015205 7.685072 4.294984 3.7349053 2.925652 4.962329 3.799215 4.361665 3.073338 3.187451
## FAM63A  4.905487 4.009917 3.683882 3.896515 4.7856232 4.552264 5.417161 4.361230 4.103027 4.575127 6.084497
## ACADS   3.521845 3.758492 3.220628 3.483945 0.9475664 1.905945 2.902085 2.096262 2.865018 2.541062 4.087720
## GMDS    5.095428 5.425335 5.134124 5.515992 4.2281563 6.193263 5.167644 6.601120 5.207890 3.069358 3.896811
##             A18S     A0CS     A0EI     A0IO     A0T6     A1AU     A07Z     A0XS     A1BD     A08T     A12Y
## RTN2    4.885975 4.812521 4.145511 4.770780 3.686174 4.234722 4.668950 5.163421 5.862224 4.492575 3.451556
## NDRG2   5.190614 5.481586 4.209690 4.894866 5.714241 6.655277 5.074468 5.716168 6.367080 5.924680 4.315363
## CCDC113 5.981202 4.514267 4.871415 4.923091 3.999832 4.978289 4.836763 3.099718 4.402046 3.565575 3.035121
## FAM63A  6.839739 5.960769 5.562853 5.903991 5.543870 5.967937 7.315990 5.370638 7.073223 6.133809 6.137805
## ACADS   3.807709 5.826708 3.213199 4.201494 3.211621 4.088356 6.577862 4.426710 4.262734 4.193605 3.455379
## GMDS    4.467859 4.661853 3.977644 4.568149 3.908653 3.413226 3.640991 3.483881 2.866784 5.025717 5.219259
##             A0J5     A18F     A0AS     A0DV     A140     A0SU     A12A     A0RM     A0AZ     A0EW     A0XW
## RTN2    3.324178 3.699449 3.147610 4.551102 3.371083 5.279948 4.599786 4.961715 4.395032 3.669192 4.060707
## NDRG2   5.204543 6.743026 3.310945 6.751697 4.767956 6.742996 6.767056 7.121645 6.166074 7.481286 3.993213
## CCDC113 3.658085 3.213309 3.392015 3.561305 4.266360 4.197921 3.613720 2.031879 4.705795 3.912063 3.859653
## FAM63A  6.019478 6.467441 3.583159 5.693453 7.680580 5.517610 6.374306 6.552616 5.685660 5.385438 5.234679
## ACADS   4.348268 3.839791 2.573175 4.361170 4.958535 3.757448 3.926513 5.375324 3.461114 4.981446 2.939582
## GMDS    2.901918 3.613409 4.553301 4.581463 2.306479 3.604445 4.316497 3.573679 3.908730 4.028187 4.368607
##             A12B     A0BP     A0RG     A0T7     A08A     A0DK     A0SH     A18N     A06P     A15L     A0YL
## RTN2    4.955273 3.946813 5.161843 3.628120 5.319757 4.229001 4.549374 5.160065 4.418414 3.003667 4.394415
## NDRG2   6.554334 6.110317 5.282558 7.041361 5.670118 6.234561 5.734280 5.743608 5.550527 5.638583 7.329557
## CCDC113 3.729381 3.599571 3.652475 4.567336 4.213460 2.876254 3.266107 3.799948 3.408737 3.767432 4.225351
## FAM63A  7.175329 5.866863 6.740858 4.849512 6.421754 6.278993 4.586105 6.548107 6.284064 5.833073 5.909271
## ACADS   3.771734 4.873476 3.834633 5.031143 6.435726 3.401421 3.781805 5.203101 4.189855 1.428122 4.124782
## GMDS    4.924317 3.476359 4.232467 3.994755 4.211985 4.533902 4.445566 3.016115 4.291386 4.561102 4.448572
##             A1AL     A133     A086     A0I8     A0EA     A09A     A0DS     A1B1     A0X0     A1AP     A0W5
## RTN2    4.318402 4.567727 3.380619 3.591457 3.934620 3.534916 5.337452 3.156414 4.318445 4.434544 4.053462
## NDRG2   7.671057 5.631257 5.348448 6.711921 6.485034 5.598355 5.431434 6.889978 5.134913 4.996163 6.324229
## CCDC113 4.058701 4.856185 2.812439 4.245995 4.373684 4.435664 3.569027 4.403957 4.249242 3.360406 4.206724
## FAM63A  6.332046 6.715817 5.614007 6.305527 6.607800 6.053269 6.544494 4.557049 6.261542 7.132167 5.686577
## ACADS   3.830086 3.637716 3.446198 3.597418 5.298255 3.821643 3.157999 3.427855 4.405081 2.979350 3.717058
## GMDS    3.988674 4.967355 3.844804 3.978552 3.381281 4.133674 3.789697 4.472276 4.407352 3.292519 4.446478
##             A0JF     A1AV     A0RO     A08Z     A0RV     A0DP     A0EX     A15R     A0FD     A0ES     A0BM
## RTN2    4.255694 4.976229 3.593910 3.338102 4.312011 4.391099 4.971500 5.829543 5.114808 4.491791 3.854894
## NDRG2   6.107624 4.682798 6.831737 4.578062 6.562096 6.629841 6.442082 6.122818 5.004968 7.224767 7.563725
## CCDC113 3.566409 5.538055 5.843992 4.027111 3.146601 4.792597 3.858766 4.058642 4.246867 4.211227 3.714711
## FAM63A  5.823695 6.984005 5.434283 5.675758 6.527390 6.071293 5.216955 6.802337 5.049330 5.603656 4.972501
## ACADS   4.724552 5.848000 1.918908 3.367570 3.087441 4.333238 3.814054 3.339114 3.457678 3.962619 4.167155
## GMDS    4.618498 5.651612 4.426422 5.717837 4.689314 4.153339 4.377855 2.615647 3.599680 4.249810 4.587572
##             A0EU     A12X     A146     A0CD     A0BQ     A04A     A0CT     A0TZ     A03L     A1AK     A0E1
## RTN2    2.760552 3.285527 2.181406 4.831567 4.930042 3.897918 5.226293 1.560674 3.682643 4.174028 3.240652
## NDRG2   4.972966 6.049840 5.570016 4.273907 6.153962 4.727599 6.574909 4.528818 4.927297 6.933249 6.032330
## CCDC113 3.250293 5.094973 4.711167 3.816242 4.304354 3.633439 1.783738 3.897716 4.111116 4.353695 3.004524
## FAM63A  5.821183 6.752349 6.352394 5.779353 6.357639 6.226870 5.881396 5.792156 4.983386 6.927104 6.454520
## ACADS   4.197412 4.716806 2.759397 5.127855 3.385413 1.853465 3.108414 3.464086 2.941760 4.921953 4.474807
## GMDS    3.129062 4.634938 3.824802 5.385437 4.917877 3.285392 1.983430 2.888763 4.328807 2.646618 5.919961
##             A0H7     A0FS     A0BS     A08O     A12H     A15E     A0W4 GO:0000122 GO:0006357 GO:0007155
## RTN2    4.286326 4.728350 3.139900 4.346977 3.287485 4.684112 4.294419          0          0          0
## NDRG2   6.206116 6.857311 6.222359 5.708690 5.043387 6.274357 5.236494          0          0          0
## CCDC113 3.897574 3.088589 4.306467 3.995944 3.665758 4.599318 4.310629          0          0          0
## FAM63A  5.390505 6.047637 6.912236 6.189790 5.943128 5.335620 5.955053          0          0          0
## ACADS   1.802260 5.754979 5.317992 4.488860 4.823124 4.247261 4.631673          0          0          0
## GMDS    3.603636 3.581223 4.686750 3.186237 5.077987 3.627571 4.648448          0          0          0
##         GO:0007165 GO:0007411 GO:0008285 GO:0016477 GO:0019221 GO:0030335 GO:0043312 GO:0045893 GO:0045944
## RTN2             0          0          0          0          0          0          0          0          0
## NDRG2            1          0          0          0          0          0          0          0          0
## CCDC113          0          0          0          0          0          0          0          0          0
## FAM63A           0          0          0          0          0          0          0          0          0
## ACADS            0          0          0          0          0          0          0          0          0
## GMDS             0          0          0          0          0          0          0          0          0
##         GO:0055114
## RTN2             0
## NDRG2            0
## CCDC113          0
## FAM63A           0
## ACADS            0
## GMDS             0
head(tar_read(annot_matrix2))
##                 A0FJ        A13E        A0G0        A0SX        A143        A0DA        A0B3       A0I2
## YWHAE     0.04913078 -0.07998211 -0.03284989 -0.20532949  0.06019021  0.03076171 -0.10786154  0.6498440
## EIF4EBP1  0.44748623  0.60521842  0.89460973 -0.14132292  0.13176899  0.03299680 -0.03712469 -0.5214866
## TP53BP1   0.91783419  0.05910121  0.51704453 -0.31372867  0.33091238 -0.22027100 -0.54474306 -1.6020354
## ARAF      0.02274147 -0.45985298 -0.19182192 -0.07482347 -0.02435747  0.41861665  0.43050350 -0.1871466
## ACACA    -0.08626782 -0.59269183  0.41117190 -0.85148060  0.76975143 -0.71430870 -0.36347405  1.0776148
## ACCB     -0.41662442 -0.06226840  0.82582859 -0.66341044  0.87347870 -0.21752677 -0.26931384  1.5899824
##                 A0RT       A131         A124        A1B6        A1AZ        A0YM        A04P        A04T
## YWHAE    -0.01365044  0.4309342 -0.102577549  0.15423052 -0.05039163  0.06663868  0.07178029 -0.12609547
## EIF4EBP1 -0.63485063  1.0525716 -0.009255264 -0.39660615  1.12550091  1.54959594 -0.14261441  0.79519820
## TP53BP1  -0.72072329 -0.8113353 -0.681091817 -0.34914824  0.24034940 -0.17552648  0.01601470  0.20713236
## ARAF     -0.37488300  0.3532624  0.070807204 -0.22111950 -0.08041112 -0.44448272  0.27759824  0.05686482
## ACACA    -1.25449108 -0.8832967  0.484237104 -0.25114128  0.07222233 -0.19200311 -0.15725206 -0.67267960
## ACCB     -0.90135358 -0.6813647  0.045396912 -0.03205812  0.33437025  0.15785199  0.07170919 -0.21057209
##                 A0AT        A0AL         A0CE          A07R        A0FL        A150        A0E0       A0U4
## YWHAE    -0.03510511  0.02031388  0.006496486  1.022935e-02 -0.02361313 -0.17057438  0.12826354  0.4117473
## EIF4EBP1  0.08817975 -0.04429098 -0.069721010 -3.997427e-05  0.91845032  0.10651340 -0.10974424  1.2536159
## TP53BP1  -0.45684808 -0.31573883  0.650410261 -8.598333e-02 -0.50578279 -0.08917507 -0.05900489 -1.1088154
## ARAF      0.07382528 -0.31804237  0.645008667  5.492385e-01  0.38690508  0.42446259  0.05793049  0.1843648
## ACACA    -0.10844835 -0.01201742  0.159326402 -7.381441e-01 -0.21117641 -0.86165684  0.28663889 -0.9652205
## ACCB     -0.20688548  0.08417570  0.359152694 -3.718771e-01 -0.02620671 -0.45189197  0.62803284 -1.1004647
##                 A0XU        A0AV       A0AR       A0RX        A0D2        A0CM       A0WX        A0T0
## YWHAE     0.07403159  0.40683769 0.17772191  0.6671865  0.07213385 -0.17250159  0.2084185 -0.16337411
## EIF4EBP1 -0.10294224 -0.04816999 0.77350218 -0.4982787  0.67030375  0.57317523 -0.1383251 -0.09672684
## TP53BP1  -0.09666688 -0.65666480 0.10875114 -0.7914337 -0.47039823  0.21967364 -0.4942531 -0.42736982
## ARAF      0.06907737 -0.30181209 0.03544246 -0.4584311 -0.11735984  0.05736489  0.1126964  0.35266129
## ACACA    -0.11755679 -0.66413755 0.23931506 -0.9456168 -0.55918956 -0.21882664 -0.8601565  0.41070905
## ACCB     -0.32518868 -0.01413711 0.69474633 -0.3431517 -0.38162147 -0.06093574 -0.4941083  0.83089602
##                 A0T2        A04U       A0JL       A147        A0B9          A1AI        A14X        A12V
## YWHAE    -0.08703159 -0.02779448 -0.2221881 -0.3602582 -0.09746623 -9.038032e-05 -0.02915253 -0.07256821
## EIF4EBP1  0.61464819  0.54281880 -0.7263554  0.2963119  0.28115435  6.590760e-01 -0.41394946  0.14103431
## TP53BP1   0.23084921  0.80963266 -0.1094235  0.1195848  1.03754786  2.063061e-01 -0.71435019 -0.17953619
## ARAF      0.34148365  0.08032620  0.1304061 -0.1486517 -0.03110734  2.986835e-01 -0.36875294 -0.06853516
## ACACA     0.19232127 -0.37590016 -0.2573800 -1.0008629 -0.60781361  2.406539e-01 -1.25448790 -1.09497374
## ACCB      0.60823231 -0.23683087 -0.0209081 -0.6103342  0.03623308  2.013784e-01 -0.79260646 -0.71765484
##                  A1AY       A0D0         A0SK       A128         A04D       A0A7        A094        A12L
## YWHAE    -0.054829765  0.3824269  0.218651975  0.3324081 -0.205548154 -0.1596453 -0.32473305 -0.04344412
## EIF4EBP1  0.007807898  0.6180407  2.348937988  0.5065296 -0.147643395 -0.2242469  0.21593275  0.38455441
## TP53BP1  -0.075287155 -0.4270996  0.005416753 -0.9711423 -0.103927214 -1.1624485 -0.05943466 -0.33648846
## ARAF      0.158501500  0.1395464 -0.068234716  0.1938066  0.006738975  0.1554911  0.49079943  0.41502360
## ACACA    -0.685292020  0.3183916 -0.850736831 -0.9275520  0.111768841 -0.1522872  1.20535055  2.07303645
## ACCB     -0.180017897 -0.3105551 -0.781911026 -1.2740621  0.357749529 -0.3142226  1.48913627  1.82543036
##                 A0I9        A0EE       A135        A152        A18P       A18R         A08X        A0TX
## YWHAE    -0.13519444  0.20855357  0.1863144 -0.35902507 -0.10696223 -0.2053096  0.009604319  0.08891257
## EIF4EBP1 -0.33349040  0.05042412 -0.6957235  0.01114068 -0.29567957  0.1540785 -0.470798283 -0.52618047
## TP53BP1  -1.24733195 -0.15774083 -0.7811252  0.03480274  1.31010433  0.2687635 -0.529870879 -0.90594068
## ARAF      0.05777585  0.51301280 -0.2032814  0.17485319 -0.04975128  0.2218992 -0.010156351  0.47239815
## ACACA     2.20804740 -0.56615145  0.2090943 -0.62119053 -0.54414221  0.1147792 -0.762491820 -0.31338439
## ACCB      2.68643899 -0.57719372  0.4523723 -0.37231047 -0.08379475  0.6008600 -0.447065964 -0.69991211
##                A09X       A1AT        A12Q        A12T        A0RH        A07I        A04W        A12P
## YWHAE    -0.1452121 -0.2137481 -0.02665069  0.02448898  0.05336191 -0.16575908  0.01732674 -0.02834328
## EIF4EBP1  0.9133893 -0.2933581  0.27107573  0.31906683 -0.46378954 -0.44816287  0.39216603  0.74462774
## TP53BP1  -0.4881384  0.4174163  0.43851075 -0.65194847 -1.41979235  0.02476909 -0.16114981 -0.11724732
## ARAF      1.0728245 -0.1423640 -0.27802677  0.03342477 -0.01921547  0.09001330  0.43137927 -0.02968595
## ACACA     1.5325083  0.5937637  1.03762278  0.32105385 -1.00276346  1.25877264  0.23361773  0.78195934
## ACCB      1.5711548  0.2055559  1.08066133 -0.08252071 -0.57105951  1.41782931 -0.19130685  0.69284338
##                 A0EQ        A0D1        A09G        A1B0        A14P        A0T1        A137        A13Z
## YWHAE    -0.01786035 -0.08492728 -0.19168728  0.21474769 -0.05799150 -0.21747907 -0.08803255  0.04933478
## EIF4EBP1 -0.24529946  1.24934075  0.06083982  0.05885925  0.47517735 -0.18302393  1.10231628  0.97598320
## TP53BP1  -0.26047282  0.38597603 -0.16245628 -0.74753567 -0.09938019  0.04312771  0.10440564  0.43356778
## ARAF     -0.24564903  0.02061657  0.14395121  0.06822545 -0.40126092  0.30801515 -0.14032776  0.19165835
## ACACA    -0.01749434 -0.95814121  1.19739063 -0.54739970 -0.39300372  1.32309400  0.37771145  0.14075020
## ACCB      0.27193951 -0.56385715  1.30890455 -0.14094375 -0.59616259  1.74511280  0.30831068 -0.06501095
##                 A08L        A0IK        A12D       A0XN        A0B0       A18S         A0CS        A0EI
## YWHAE    -0.30622577  0.49932334 -0.16633329  0.2645818  0.16583752 -0.1594390 -0.022463404  0.14154974
## EIF4EBP1 -0.05871105 -0.31424236 -0.25664719  0.9454482 -0.62007726  0.7811332  0.097860488  0.79883067
## TP53BP1  -0.19369904 -1.26675743  0.03191129 -0.2737528  0.08543817  0.6475790 -0.001748506  0.09620899
## ARAF      0.19365136 -0.03038972 -0.12319996 -0.3084782  0.11688457  0.1303308  0.334964464 -0.09385336
## ACACA     0.15529593 -1.57896525 -0.15933744 -0.2625758 -0.03561580  0.2899688  0.749944295 -1.21085371
## ACCB      0.52746407 -1.01851966 -0.38789434 -0.3747893  0.35980241  0.8081174  0.981050852 -0.77786324
##                 A0IO        A0T6        A1AU       A07Z        A0XS       A1BD        A08T         A12Y
## YWHAE     0.08642076  0.10550155  0.37996457 -0.4678713  0.08678585 -0.1289187 -0.07846243 -0.139624632
## EIF4EBP1 -0.65464641  0.18094438  0.33115039 -0.6534718 -0.62969677 -0.2848388  0.15330913 -0.155897261
## TP53BP1   0.24605366  0.19713456 -0.09354243  0.3289483 -0.03750029  0.5523604  0.29559472  0.280028069
## ARAF     -0.12354224 -0.34896948 -0.55963733  0.1544671  0.04171820  0.1172685  0.14778960  0.002036919
## ACACA    -0.17369193 -0.28008209  0.77103294  2.2279160 -1.07151387 -0.0161823 -0.43791724  0.150767232
## ACCB     -0.55539035 -0.05912806  0.03904519  2.4836557 -0.66809161  0.2107903 -0.30475747  0.198280480
##                 A0J5        A18F        A0AS        A0DV        A140        A0SU         A12A        A0RM
## YWHAE    -0.21552677  0.09568197 -0.04635576  0.45259573 -0.19219433  0.02704793 -0.152233346  0.07891276
## EIF4EBP1 -0.60762880 -0.12126500 -0.19201165 -0.28018656 -0.38325583 -0.13660724 -0.229133813  0.26233805
## TP53BP1  -0.05888632 -0.26453804  0.17448861 -0.27528775 -0.03076983  0.15716694  0.262321295 -0.19091957
## ARAF      0.46568117 -0.02355888 -0.08826188 -0.08613218  0.01456160 -0.04209240  0.003812493 -0.49300086
## ACACA    -0.72991851 -0.03039667  0.89393507 -0.51919125  0.92510859  0.45384257 -0.688932842 -0.63912745
## ACCB     -0.62076963 -0.13891954  0.91059564 -0.69367323  1.20033224  0.30185448 -0.261832300 -0.32742498
##                 A0AZ        A0EW       A0XW        A12B       A0BP         A0RG        A0T7       A08A
## YWHAE     0.44813177  0.24075610 -0.1921050  0.28809052  0.6142197  0.006611735  0.09425692 -0.2893167
## EIF4EBP1 -0.07537384  0.95510271 -0.2249715  0.28751521 -0.3370092 -0.266905610  0.15714997 -0.2902958
## TP53BP1  -0.23187084  0.01356203  0.4909079  0.01666412 -0.1732544  0.235397041 -0.10476700  0.7068535
## ARAF      0.36733354 -0.15248756 -0.2215480 -0.09751097 -0.2412493 -0.169662569 -0.17345254  0.1496799
## ACACA    -0.19927512 -0.62426734  1.1461389  0.40130928  1.0064003  0.062619936  0.39504278  0.6492362
## ACCB     -0.86401722 -0.38855134  0.9585337 -1.12405209  1.0776383  0.405224079 -0.40038358  1.1057882
##                  A0DK       A0SH        A18N       A06P        A15L        A0YL        A1AL         A133
## YWHAE     0.208312992 -0.2146377  0.02057174  0.5320804  0.24446389  0.02441686  0.25962881  0.233985222
## EIF4EBP1  0.006902877 -0.0348712 -0.47094946  0.3974088  0.35611833  0.31565682 -0.47644956  0.001715192
## TP53BP1   0.461756644 -0.2300382  0.33733423 -0.4671832  0.46874689  0.48026692 -0.05283317 -0.539913732
## ARAF     -0.083873409  0.2163685 -0.13868696 -0.1757303 -0.16117601 -0.36611220 -0.45663158 -0.130470151
## ACACA     0.243873461  1.3612271 -0.65434685 -0.0199524  0.06804862 -0.40401486 -0.10943659  0.068201372
## ACCB     -0.609707357  1.5125324 -0.17100515  0.2557449 -0.03833923  0.02396029  0.08630307  0.186355403
##                 A086       A0I8        A0EA       A09A        A0DS        A1B1       A0X0        A1AP
## YWHAE    -0.06022245  0.2593484  0.27887146  0.1501800  0.08160479  0.12138451 -0.1459906  0.06991067
## EIF4EBP1  0.43571413  0.3529033 -0.52845711  0.3721886  0.32026039  0.02523423 -0.2877079 -0.02022466
## TP53BP1  -0.22378107 -0.4190778  0.30041806 -0.3300114  0.21959367 -0.46314039  0.7142044  0.33062720
## ARAF     -0.03175502 -0.1608799 -0.02967306  0.3415218 -0.13344800 -0.23412186 -0.1183153 -0.40823958
## ACACA     0.43090563  1.5458696 -0.13707113  0.4368219 -0.94325459 -0.78851367  0.4255080 -0.67741788
## ACCB      0.96868828  0.8709450  0.18134112  0.4566380 -0.77731483 -0.49408623  0.6665537 -0.74875727
##                  A0W5         A0JF         A1AV        A0RO        A08Z       A0RV        A0DP        A0EX
## YWHAE    -0.068143509 -0.082361654 -0.008565319  0.20073233  0.21562355  0.1174676  0.61208279  0.19225553
## EIF4EBP1 -0.361338800 -0.289923833 -0.359263948 -0.09592371 -0.11602150  0.8533835 -0.24256401  0.16823552
## TP53BP1   0.255844248  0.006400965  0.645392566  0.22659302  0.09092303  0.2852072 -0.48847031 -0.36727570
## ARAF     -0.008508998  0.234631425 -0.218606460 -0.09025331  0.09592512 -0.3121126 -0.09959578 -0.11410952
## ACACA    -0.378758677  0.070230030  0.821756843  0.30810017 -0.42072622 -1.2115732  0.16090718 -0.25781609
## ACCB     -0.601903890  0.324889398  0.884751097  0.83381913 -0.01180335 -0.8640820  0.75451871 -0.05032689
##                A15R          A0FD         A0ES         A0BM       A0EU        A12X        A146        A0CD
## YWHAE    0.15951372 -0.0003992998  0.331390028  0.234077379  0.6602348  0.01399538 -0.12540871 -0.10988943
## EIF4EBP1 1.43036763  0.3021787216  0.777901151 -0.044702482 -0.3887336  2.04807978 -0.12822238 -0.40588993
## TP53BP1  1.19168757  0.7830962010 -0.179800997  0.249263206 -0.4445914  0.46757149  0.18580518 -0.26228104
## ARAF     0.10669297 -0.0353334053 -0.007782728  0.008670462 -0.1844897 -0.43438697  0.53235978  0.08775629
## ACACA    0.43827642  0.1019272573 -0.062342374  0.517704430 -0.4002549  0.39724306  0.06463656  0.59588277
## ACCB     0.03445577 -0.7286720277  0.217673154  0.845228991 -0.4984337  0.43535304  0.28106347  0.73116503
##                 A0BQ        A04A        A0CT       A0TZ        A03L        A1AK       A0E1       A0H7
## YWHAE     0.29664725 -0.10341419 -0.01271869  0.2534825 -0.06255032 -0.00628647  0.4900114  0.6085458
## EIF4EBP1 -0.34952985  0.37093698  0.23785158 -0.3171774  0.02082981 -0.29036200 -0.1878629 -0.4059596
## TP53BP1  -0.35319591  0.58863472 -0.83354244 -0.2604502 -0.20783825  0.01482852 -0.1164977 -0.7563690
## ARAF     -0.03755203 -0.02265695 -0.18495062 -0.1670993  0.05328247 -0.23236417 -0.2357682 -0.2125003
## ACACA     2.09181497 -0.47350147  1.16285497 -0.0904107 -0.16965978  0.66700812 -0.4736231 -1.2983173
## ACCB      1.43110561 -1.05352669  1.22102621 -0.1402257 -0.36904927  0.53386343 -0.5331481 -0.3960725
##                 A0FS        A0BS         A08O        A12H        A15E        A0W4 GO:0000082 GO:0000122
## YWHAE     0.28588916  0.10558917 -0.082599309  0.04428213 -0.08457028 -0.01095410          0          0
## EIF4EBP1 -0.70731155  0.35069685 -0.434463492 -0.45207404 -0.24924165 -0.34544615          1          0
## TP53BP1   0.19350409  0.58851125 -0.113726155  1.16034608  0.58585849  0.44976669          0          0
## ARAF     -0.29306315  0.23146311 -0.005437017 -0.26354606  0.18079844  0.06987084          0          0
## ACACA    -0.31986613  0.68697199 -0.098271102  0.54047479  1.38595816 -0.30662370          0          0
## ACCB     -0.08705945 -0.03232127 -0.373714666  0.69083131  0.95161707 -0.18940735          0          0
##          GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001701 GO:0001934 GO:0006357 GO:0006367 GO:0006468
## YWHAE             1          0          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          0          0          0          0          0          0          0          0
## ARAF              1          0          0          0          0          0          0          0          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0006915 GO:0006974 GO:0006977 GO:0007050 GO:0007155 GO:0007165 GO:0007169 GO:0007411 GO:0007507
## YWHAE             0          0          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          1          0          0          0          0          0          0          0
## ARAF              0          0          0          0          0          0          0          0          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0007568 GO:0008283 GO:0008284 GO:0008285 GO:0010468 GO:0010628 GO:0010629 GO:0016032 GO:0016579
## YWHAE             0          0          0          0          0          0          0          1          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          0          0          0          0          0          0          0          0
## ARAF              0          0          0          0          0          0          0          0          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0018105 GO:0018107 GO:0018108 GO:0019221 GO:0030154 GO:0030335 GO:0032355 GO:0032869 GO:0033138
## YWHAE             0          0          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          0          0          0          0          0          0          0          0
## ARAF              0          0          0          0          0          0          0          0          1
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0033674 GO:0035556 GO:0042060 GO:0042127 GO:0042493 GO:0042981 GO:0043065 GO:0043066 GO:0045471
## YWHAE             0          1          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          1
## TP53BP1           0          0          0          0          0          0          0          0          0
## ARAF              0          0          0          0          0          0          0          1          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0045892 GO:0045893 GO:0045944 GO:0046777 GO:0048538 GO:0050821 GO:0051091 GO:0051897 GO:0070374
## YWHAE             0          0          0          0          0          0          0          0          0
## EIF4EBP1          0          0          0          0          0          0          0          0          0
## TP53BP1           0          1          1          0          0          0          1          0          0
## ARAF              0          0          0          0          0          0          0          0          0
## ACACA             0          0          0          0          0          0          0          0          0
## ACCB              0          0          0          0          0          0          0          0          0
##          GO:0071456 GO:0090090 GO:0098609 GO:1901796 GO:2001244
## YWHAE             0          0          0          0          0
## EIF4EBP1          1          0          0          0          0
## TP53BP1           0          0          0          0          0
## ARAF              0          0          0          0          0
## ACACA             0          0          0          0          0
## ACCB              0          0          0          0          0
p <- heatmaply(categ_matrix1, 
        dendrogram = "none",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(categ_matrix1),
        labRow = rownames(categ_matrix1),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")
p <- heatmaply(categ_matrix2, 
        dendrogram = "none",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(categ_matrix2),
        labRow = rownames(categ_matrix2),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")

Expanded Matrices

Gene Ontology used: BP

Min. number of genes applied to filter: 8

Annotated categories: 13 (for data/mrna.csv)

Annotated categories: 61 (for data/prots.csv)

Features+Categs in ROWS: 213 (for data/mrna.csv)

Features+Categs in ROWS: 172 (for data/prots.csv)

Samples in COLUMNS: 150 (for data/mrna.csv)

Samples in COLUMNS: 150 (for data/prots.csv)

(Showing only partial output)

tail(tar_read(expd_matrix1), ncol(categ_matrix1))[,1:6]
##                A0FJ     A13E     A0G0     A0SX     A143     A0DA
## GO:0000122 4.975514 5.014288 4.354496 5.287829 4.388574 4.703340
## GO:0006357 5.358933 5.651490 5.159456 5.959377 5.084826 5.487008
## GO:0007155 6.068514 5.938148 6.008194 6.606449 5.609092 6.493687
## GO:0007165 5.190907 5.179589 5.086928 5.896685 4.964933 5.289600
## GO:0007411 5.209696 4.911230 5.568726 6.002954 5.247555 5.849531
## GO:0008285 4.850748 5.628700 5.559798 6.196543 5.559160 5.732965
## GO:0016477 4.467429 5.545002 6.084154 6.342951 6.550521 6.424268
## GO:0019221 4.285585 4.339224 4.442392 6.117472 5.362300 5.306170
## GO:0030335 4.940894 4.526876 5.186276 5.923001 4.685379 5.340370
## GO:0043312 5.256378 4.540444 5.513148 5.530951 5.754397 4.984525
## GO:0045893 4.945589 4.911753 4.797016 5.473086 5.192641 4.559235
## GO:0045944 5.014163 5.063401 4.732361 5.710688 5.062169 5.162256
## GO:0055114 4.507878 4.414600 4.918826 4.932707 4.894436 4.802867
tail(tar_read(exc_exp_mat1), ncol(categ_matrix1))[,1:6]
##                A0FJ     A13E     A0G0     A0SX     A143     A0DA
## GO:0016477 4.467429 5.545002 6.084154 6.342951 6.550521 6.424268
## GO:0043312 5.256378 4.540444 5.513148 5.530951 5.754397 4.984525
## GO:0055114 4.507878 4.414600 4.918826 4.932707 4.894436 4.802867
dim(tar_read(exc_exp_mat1))
## [1]   3 150
tail(tar_read(expd_matrix2), ncol(categ_matrix2))[,1:6]
##                   A0FJ         A13E          A0G0         A0SX          A143         A0DA
## GO:0000082  0.08489980  0.336677822  0.1119364371  0.132907983  0.2131787559  0.072103768
## GO:0000122 -0.27482556 -0.147144823 -0.4183629026 -0.292259414 -0.2973200923 -0.336981518
## GO:0000165  0.07622744  0.189509183  0.1256605044  0.058991557  0.1196075280  0.097879156
## GO:0000187 -0.02372494  0.191530915  0.2009855473  0.322285592 -0.0869276571  0.224646972
## GO:0001525  0.13043805 -0.129834380 -0.0921494909  0.268844404 -0.3373306412 -0.017102932
## GO:0001666  0.08944101 -0.140874501 -0.2420583339  0.140057794 -0.1545093549 -0.278546050
## GO:0001701 -0.08369993 -0.117808693 -0.2400020828 -0.262398372 -0.1063332010 -0.207672715
## GO:0001934  0.22167378 -0.071793185  0.0059517080 -0.004695533  0.3786330061 -0.026809124
## GO:0006357 -0.44105207  0.018582923 -0.4456880716 -0.107618121 -0.1794351142 -0.263030185
## GO:0006367 -0.37807640 -0.217422477 -0.4515217890 -0.382301742 -0.4628282752 -0.402502336
## GO:0006468  0.04384241 -0.012195461  0.0686075696  0.214935373  0.0561904289 -0.013535358
## GO:0006915  0.12761670 -0.026639992 -0.1342128706  0.210012976 -0.0324969741 -0.062760267
## GO:0006974  0.18917421 -0.033450403  0.1404693246  0.055255983 -0.1910492830  0.008739606
## GO:0006977  0.33058430  0.274551206  0.2575656626  0.360402894  0.3617389207 -0.084608669
## GO:0007050  0.03441458  0.292665738  0.0556843231  0.291426874  0.1417121906  0.177136263
## GO:0007155 -0.06441327  0.006709432 -0.0339015759 -0.159775692 -0.0679366169  0.150489660
## GO:0007165 -0.27900782 -0.266694235 -0.1644668807 -0.110421310 -0.2506492541 -0.263054266
## GO:0007169  0.07685028  0.523227325  0.5631833767  0.365590109  0.1999179038  0.113374476
## GO:0007411 -0.09898379  0.331088481  0.3261074003 -0.064801905 -0.1738483420 -0.147993794
## GO:0007507 -0.02032936  0.111431770 -0.0285711480  0.158872521  0.0991334224  0.118190996
## GO:0007568  0.07790115 -0.420646638  0.1032335058 -0.001736004  0.0086647605 -0.102973234
## GO:0008283  0.03679451 -0.144167148  0.0255178996 -0.111399009  0.0840318788 -0.052401503
## GO:0008284  0.08482870  0.257111457  0.0005207242  0.197894491 -0.0236297526  0.022160249
## GO:0008285 -0.11138998 -0.166885018 -0.1626436833 -0.211962199 -0.1376858891 -0.105234086
## GO:0010468  0.01125860 -0.153391521 -0.2176228032 -0.007971024 -0.4203021508 -0.054905609
## GO:0010628 -0.00122858 -0.098698107 -0.1055718003  0.066310240 -0.1366106255  0.080458342
## GO:0010629 -0.23619110 -0.028785330 -0.3892505117 -0.223956091 -0.3021354399 -0.240027932
## GO:0016032 -0.07457173 -0.010786512  0.0914214747  0.048616664  0.0438110215  0.009434538
## GO:0016579 -0.48380275 -0.365095246 -0.6127620199 -0.333712327 -0.6224947667 -0.506192428
## GO:0018105  0.06317664 -0.117787592 -0.0358040097  0.247075359 -0.0503240522 -0.033782045
## GO:0018107  0.16622397 -0.052166874 -0.1429365756  0.216677404 -0.1240914732  0.003439253
## GO:0018108  0.03007974  0.268677229  0.1898227851  0.418797935  0.1536240352  0.089635663
## GO:0019221 -0.06805777  0.173421854 -0.0334762431  0.172616196 -0.4219052089  0.208626430
## GO:0030154  0.06266369 -0.017867445 -0.0586608115  0.202329129  0.3572727979 -0.055773142
## GO:0030335  0.07092124  0.345829604 -0.1007203072  0.418595430  0.1003942279 -0.064002287
## GO:0032355 -0.34406908 -0.446365697 -0.1666957447 -0.529643452 -0.6018513487 -0.370357956
## GO:0032869  0.24803647 -0.180192879 -0.0891644310  0.224420710  0.1584007938  0.029553808
## GO:0033138  0.36210715 -0.283654291 -0.5135656042  0.095601671  0.2240143146 -0.249247057
## GO:0033674  0.05309816  0.366930337  0.1290877119  0.185115483  0.1810435065  0.034244876
## GO:0035556 -0.04198901 -0.065201822 -0.0669765327 -0.043429659  0.0104424180 -0.005881260
## GO:0042060  0.05087015  0.006398232 -0.0453615084  0.004516628  0.4749383469  0.133403389
## GO:0042127 -0.06461140  0.352299355  0.3414221430  0.629645793 -0.2558531062  0.306249681
## GO:0042493  0.10065786 -0.100860898  0.0719475904 -0.068457753 -0.1113006377 -0.067164409
## GO:0042981 -0.38891545 -0.314969068 -0.4301307672 -0.186592306 -0.3627193499 -0.306987364
## GO:0043065 -0.06841879 -0.177206068 -0.0437627994 -0.095497340 -0.0089997349  0.064977860
## GO:0043066  0.17748119  0.084221187  0.0446931651  0.087754375  0.0674620117  0.083559240
## GO:0045471 -0.20824125 -0.132666688 -0.1576763043 -0.182859533 -0.2209665652 -0.224879055
## GO:0045892 -0.07322803  0.196502210  0.0960542524 -0.179838876  0.1453523156  0.098838332
## GO:0045893 -0.17324920 -0.177955202 -0.1334929204 -0.271777012 -0.0048038792 -0.177876574
## GO:0045944 -0.19587062 -0.084388027 -0.1659883857 -0.138425902 -0.0438597330 -0.109792850
## GO:0046777  0.21686266  0.226945389  0.2381816961  0.228248405  0.4362714716  0.093550313
## GO:0048538 -0.09674308 -0.440442887 -0.3333299382 -0.136174964 -0.4601796000 -0.262351567
## GO:0050821  0.26731790 -0.077598349 -0.0925007853  0.064325005 -0.0006906611  0.101583260
## GO:0051091 -0.31695970 -0.073274211 -0.3805173383 -0.425677409 -0.5235161696 -0.167380867
## GO:0051897 -0.44175817 -0.119354152 -0.3978241519 -0.221571036 -0.2969110597 -0.383017751
## GO:0070374  0.29051323  0.317418294  0.1340562890  0.169023275  0.6261227595  0.125945184
## GO:0071456  0.41857396  0.092164299  0.0413925417  0.164705551  0.0884956352  0.061850564
## GO:0090090  0.09997505 -0.334316780 -0.3138133989 -0.005110155 -0.2443231857 -0.274596166
## GO:0098609  0.21100026 -0.098915205  0.1107148763 -0.116176166  0.2025518820 -0.012399848
## GO:1901796  0.05604931 -0.090767252  0.0890972070  0.199254450 -0.0493431138 -0.020527543
## GO:2001244  0.21073007 -0.231262473 -0.6335138888  0.361176457 -0.5217544145 -0.369090924
tail(tar_read(exc_exp_mat2), ncol(categ_matrix2))[,1:6]
##                   A0FJ         A13E          A0G0         A0SX          A143         A0DA
## GO:0000082  0.08489980  0.336677822  0.1119364371  0.132907983  0.2131787559  0.072103768
## GO:0000165  0.07622744  0.189509183  0.1256605044  0.058991557  0.1196075280  0.097879156
## GO:0000187 -0.02372494  0.191530915  0.2009855473  0.322285592 -0.0869276571  0.224646972
## GO:0001525  0.13043805 -0.129834380 -0.0921494909  0.268844404 -0.3373306412 -0.017102932
## GO:0001666  0.08944101 -0.140874501 -0.2420583339  0.140057794 -0.1545093549 -0.278546050
## GO:0001701 -0.08369993 -0.117808693 -0.2400020828 -0.262398372 -0.1063332010 -0.207672715
## GO:0001934  0.22167378 -0.071793185  0.0059517080 -0.004695533  0.3786330061 -0.026809124
## GO:0006367 -0.37807640 -0.217422477 -0.4515217890 -0.382301742 -0.4628282752 -0.402502336
## GO:0006468  0.04384241 -0.012195461  0.0686075696  0.214935373  0.0561904289 -0.013535358
## GO:0006915  0.12761670 -0.026639992 -0.1342128706  0.210012976 -0.0324969741 -0.062760267
## GO:0006974  0.18917421 -0.033450403  0.1404693246  0.055255983 -0.1910492830  0.008739606
## GO:0006977  0.33058430  0.274551206  0.2575656626  0.360402894  0.3617389207 -0.084608669
## GO:0007050  0.03441458  0.292665738  0.0556843231  0.291426874  0.1417121906  0.177136263
## GO:0007169  0.07685028  0.523227325  0.5631833767  0.365590109  0.1999179038  0.113374476
## GO:0007507 -0.02032936  0.111431770 -0.0285711480  0.158872521  0.0991334224  0.118190996
## GO:0007568  0.07790115 -0.420646638  0.1032335058 -0.001736004  0.0086647605 -0.102973234
## GO:0008283  0.03679451 -0.144167148  0.0255178996 -0.111399009  0.0840318788 -0.052401503
## GO:0008284  0.08482870  0.257111457  0.0005207242  0.197894491 -0.0236297526  0.022160249
## GO:0010468  0.01125860 -0.153391521 -0.2176228032 -0.007971024 -0.4203021508 -0.054905609
## GO:0010628 -0.00122858 -0.098698107 -0.1055718003  0.066310240 -0.1366106255  0.080458342
## GO:0010629 -0.23619110 -0.028785330 -0.3892505117 -0.223956091 -0.3021354399 -0.240027932
## GO:0016032 -0.07457173 -0.010786512  0.0914214747  0.048616664  0.0438110215  0.009434538
## GO:0016579 -0.48380275 -0.365095246 -0.6127620199 -0.333712327 -0.6224947667 -0.506192428
## GO:0018105  0.06317664 -0.117787592 -0.0358040097  0.247075359 -0.0503240522 -0.033782045
## GO:0018107  0.16622397 -0.052166874 -0.1429365756  0.216677404 -0.1240914732  0.003439253
## GO:0018108  0.03007974  0.268677229  0.1898227851  0.418797935  0.1536240352  0.089635663
## GO:0030154  0.06266369 -0.017867445 -0.0586608115  0.202329129  0.3572727979 -0.055773142
## GO:0032355 -0.34406908 -0.446365697 -0.1666957447 -0.529643452 -0.6018513487 -0.370357956
## GO:0032869  0.24803647 -0.180192879 -0.0891644310  0.224420710  0.1584007938  0.029553808
## GO:0033138  0.36210715 -0.283654291 -0.5135656042  0.095601671  0.2240143146 -0.249247057
## GO:0033674  0.05309816  0.366930337  0.1290877119  0.185115483  0.1810435065  0.034244876
## GO:0035556 -0.04198901 -0.065201822 -0.0669765327 -0.043429659  0.0104424180 -0.005881260
## GO:0042060  0.05087015  0.006398232 -0.0453615084  0.004516628  0.4749383469  0.133403389
## GO:0042127 -0.06461140  0.352299355  0.3414221430  0.629645793 -0.2558531062  0.306249681
## GO:0042493  0.10065786 -0.100860898  0.0719475904 -0.068457753 -0.1113006377 -0.067164409
## GO:0042981 -0.38891545 -0.314969068 -0.4301307672 -0.186592306 -0.3627193499 -0.306987364
## GO:0043065 -0.06841879 -0.177206068 -0.0437627994 -0.095497340 -0.0089997349  0.064977860
## GO:0043066  0.17748119  0.084221187  0.0446931651  0.087754375  0.0674620117  0.083559240
## GO:0045471 -0.20824125 -0.132666688 -0.1576763043 -0.182859533 -0.2209665652 -0.224879055
## GO:0045892 -0.07322803  0.196502210  0.0960542524 -0.179838876  0.1453523156  0.098838332
## GO:0046777  0.21686266  0.226945389  0.2381816961  0.228248405  0.4362714716  0.093550313
## GO:0048538 -0.09674308 -0.440442887 -0.3333299382 -0.136174964 -0.4601796000 -0.262351567
## GO:0050821  0.26731790 -0.077598349 -0.0925007853  0.064325005 -0.0006906611  0.101583260
## GO:0051091 -0.31695970 -0.073274211 -0.3805173383 -0.425677409 -0.5235161696 -0.167380867
## GO:0051897 -0.44175817 -0.119354152 -0.3978241519 -0.221571036 -0.2969110597 -0.383017751
## GO:0070374  0.29051323  0.317418294  0.1340562890  0.169023275  0.6261227595  0.125945184
## GO:0071456  0.41857396  0.092164299  0.0413925417  0.164705551  0.0884956352  0.061850564
## GO:0090090  0.09997505 -0.334316780 -0.3138133989 -0.005110155 -0.2443231857 -0.274596166
## GO:0098609  0.21100026 -0.098915205  0.1107148763 -0.116176166  0.2025518820 -0.012399848
## GO:1901796  0.05604931 -0.090767252  0.0890972070  0.199254450 -0.0493431138 -0.020527543
## GO:2001244  0.21073007 -0.231262473 -0.6335138888  0.361176457 -0.5217544145 -0.369090924
dim(tar_read(exc_exp_mat2))
## [1]  51 150
tail(tar_read(int_exp_mat), 10)[,1:6]
##                A0FJ     A13E     A0G0     A0SX     A143     A0DA
## GO:0000122 2.350344 2.433572 1.968067 2.497785 2.045627 2.183179
## GO:0006357 2.458940 2.835037 2.356884 2.925879 2.452696 2.611989
## GO:0007155 3.002050 2.972429 2.987146 3.223337 2.770578 3.322088
## GO:0007165 2.455950 2.456448 2.461231 2.893132 2.357142 2.513273
## GO:0007411 2.555356 2.621159 2.947417 2.969076 2.536853 2.850768
## GO:0008285 2.369679 2.730908 2.698577 2.992290 2.710737 2.813866
## GO:0019221 2.108764 2.256323 2.204458 3.145044 2.470198 2.757398
## GO:0030335 2.505908 2.436353 2.542778 3.170798 2.392886 2.638184
## GO:0045893 2.386170 2.366899 2.331761 2.600655 2.593919 2.190679
## GO:0045944 2.409146 2.489506 2.283186 2.786131 2.509154 2.526232
dim(tar_read(int_exp_mat))
## [1]  10 150

Heatmap (of intersect matrix, after expansion)

Features+Categs in ROWS; Samples in COLUMNS

p <- heatmaply(int_exp_mat, 
        #dendrogram = "row",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(int_exp_mat),
        labRow = rownames(int_exp_mat),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")

Heatmap (after row expansion)

Features+Categs in ROWS; Samples in COLUMNS

p <- heatmaply(expd_matrix1, 
        #dendrogram = "row",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(expd_matrix1),
        labRow = rownames(expd_matrix1),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")
p <- heatmaply(expd_matrix2, 
        #dendrogram = "row",
        xlab = "", ylab = "", 
        main = "",
        scale = "none",
        margins = c(60,100,40,20),
        #grid_color = "white",
        #grid_width = 0,
        titleX = FALSE,
        hide_colorbar = FALSE,
        branches_lwd = 0.1,
        label_names = c("Feature", "Sample", "Value"),
        fontsize_row = 5, fontsize_col = 5,
        labCol = colnames(expd_matrix2),
        labRow = rownames(expd_matrix2),
        heatmap_layers = theme(axis.line=element_blank())
        )
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")

MFA Data prep

NumSamples: 150

NumGenes: 200

NumProts: 111

numGOsInGenes: 3

numGOsInProts: 51

numGOsInCommon: 10

## [1] 200 111
## [1] 200 111   3  51  10
##   [1] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal
##  [18] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal
##  [35] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Her2  Her2  Her2  Her2  Her2  Her2 
##  [52] Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2  Her2 
##  [69] Her2  Her2  Her2  Her2  Her2  Her2  Her2  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA 
##  [86] LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA 
## [103] LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA 
## [120] LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA 
## [137] LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA  LumA 
## Levels: Basal Her2 LumA
## 
## Basal  Her2  LumA 
##    45    30    75

supplementary groups: 3, 4, 5

## [1] "genes"       "prots"       "geneAnots"   "protAnots"   "commonAnots"
## [1] "c" "c" "c" "c" "c"